paml.readme July 1997
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PAML (for Phylogentic Analysis by Maximum Likelihood) contains a few
programs for model fitting and phylogenetic tree reconstruction using
nucleotide or amino-acid sequence data. The programs were written in
ANSI C and tested on UNIX systems, although PowerMac excutables are
also supplied. The UNIX commands for compiling the programs using the
GNU gcc compiler and the SUN acc compiler are listed in two files
named paml.gcc and paml.acc, respectively. Type "source paml.gcc" or
"source paml.acc" to compile. The documentation is paml1_3.doc,
prepared using Microsoft Word 6.0 for the Mac (with Equation Editor
2.0), which is supposed to be compatible with Microsoft Word 6.0 for
Windows. You should print out a copy. Bug fixes since preparation of
the document is reported in a file called paml.bugfix, to be included
with updates of the package. A web page is also constructed for the
package; the address is http://mw511.biol.berkeley.edu/ziheng/paml.html.
The package can be obtained from ftp.bio.indiana.edu (129.79.225.25)
under the subdirectory Incoming/ or molbio/evolve by anonymous ftp
(binary). It is also available from the web pge. After getting the
file paml1.3.tar.Z, you should use the following commands to decode
it:
uncompress paml1.3.tar.Z
tar xf paml1.3.tar
I used the following commands to archive and compress the files:
tar cf paml1.3.tar *
compress paml1.3.tar
PAML is distributed free of charge for academic use only. Comments
and suggestions are appreciated. If you hope to receive update
notices, please give me your email number.
Ziheng Yang
Department of Integrative Biology Email: ziheng@mws4.biol.berkeley.edu
University of California Phone: (510) 643 6299
Berkeley, CA 94720-3140 Fax: (510) 643 6264
http://mw511.biol.berkeley.edu/ziheng/ziheng.html
http://mw511.biol.berkeley.edu/ziheng/paml.html